Re: [Ifeffit] Peakfitting CeO2 data in Athena

[Stephanie Laga]

Thank you Matthew and Matt for your responses. Sorry if these are silly
questions...so then does that mean arctan and gaussian shouldn't be used
together?

What was meant by "it does not inherently include any understanding of what
that peak is"? That these functions aren't representative of the processes
occuring because the single electronic assumption doesn't hold anymore...ie
there are many electron effects once we get in the EXAFS region?

And if I am primarily looking at XANES, I don't need to be worried about
the initial EXAFS region right?

On Thu, Dec 8, 2016 at 10:48 AM, Matthew Marcus  wrote:

> The usual justification for using gaussians for peaks, aside from "it
> works" is that there's inhomogeneous broadening over and above the
> lifetime.  The usual justification for using an arctan for the step is
> exactly the opposite.  Instrument broadening is often taken to be
> gaussian.  Net result:  A (pseudo)Voight for peaks often works.  One
> issue is what to do about the post-white-line peaks, which sometimes
> are viewed as the first EXAFS wiggles.  Manceau has a nice paper about
> S XANES  (I don't have the ref handy right now) in which he goes
> through peak fitting and evaluates its uniqueness.
>mam
>
> On Thu, Dec 8, 2016 at 5:40 AM, Matt Newville
>  wrote:
> > Hi Stephanie,
> >
> >
> >
> > On Wed, Dec 7, 2016 at 12:33 PM, Stephanie Laga  >
> > wrote:
> >>
> >> Dear all,
> >>
> >> I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS
> data.
> >> I have been using moved the peak fitting function in Athena to model the
> >> XANES with an arctan background function and a series of gaussians.
> >>
> >> Looking through the literature I haven't seen too many specifics to
> using
> >> this approach (rationale for choosing the widths of peaks or how to
> define
> >> the background function). Similarly, doesn't seem to be much rationale
> for
> >> choosing a 4 vs 5 peak fit for the XANES.
> >>
> >> My main question is then...1) Is there a rational for picking the
> >> background function, specifically the height and width (can I let the
> height
> >> vary or should I be keeping a constant arctan through all samples)?
> >>
> >> Any advice is greatly appreciated!
> >>
> >> Stephanie
> >>
> >
> > Matthew answered quickly, but sort of changed the subject, suggesting a
> > different analysis (LSQ) and then discussing some of the pitfalls of that
> > approach.  Your original question is still worth discussing.
> >
> > There is not a whole lot of justification in using one particular shape
> for
> > the background.  A step broadened as arctan, error function are common
> and
> > seem to work well. Each has some theoretical explanation in that the
> > integral of a series of Lorentzian gives an arc-tangent function while
> the
> > integral of a series of Gaussians will give the error function. (If this
> is
> > wrong, can someone please correct?).  If you think as the above edge
> > spectrum as a series of finely spaced individual transitions, then these
> > functions have some justification.Whether it actually works well in
> > detail on a particular spectrum is a separate question.   FWIW, I've also
> > seen people use (successfully) a single, very broad Lorentzian for the
> "main
> > edge".
> >
> > The use of Lorentzians, Gaussians, Voigts, and PseudoVoigts is somewhat
> more
> > justified in that those are how you would expect a single electronic
> > transition to appear, especially broadened in the way(s) you'd expect a
> > monochromatic X-ray beam to be energy broadened.  Using such functions is
> > essentially asserting that there is a single electronic transition at
> that
> > energy, and you want to know it's size and shape.  This is not wrong,
> but it
> > does not inherently include any understanding of what that peak is. For
> > pre-edge peaks, it's pretty well-justified, and works pretty well.  For
> > peaks on or after the main edge or "white line", it's less justified
> because
> > we know that EXAFS-like effects can be important.
> >
> > The biggest dangers in the peak-fitting approach are:
> >1) one always gets an answer, and that is rarely "no, this is not the
> > right model to use".  In fairness, most linear algebra methods used for
> > XANES analysis or really most other spectroscopies have the same feature.
> >2) interpretation of the results can be challenging, or at least it is
> > hard to know when they are misleading.  Again, most linear algebra
> methods
> > used for XANES analysis or really most other spectroscopies have the same
> > feature.
> >3) it can sort of willfully ignore other parts of the spectra.  In
> > fairness, we all do this sort of thing all the time.
> >
> > Hope that helps.  Peak fitting is not exactly "theoretical XANES
> analysis",
> > but it is not always done in an ad-hoc manner out of ignorance either.
> >
> > Linear algebra techniques are completely justified too.
> >
> > Hope that helps,
> >
> > --Matt Newville
> >
> >

Re: [Ifeffit] Peakfitting CeO2 data in Athena

[Matthew Marcus]

The usual justification for using gaussians for peaks, aside from "it
works" is that there's inhomogeneous broadening over and above the
lifetime.  The usual justification for using an arctan for the step is
exactly the opposite.  Instrument broadening is often taken to be
gaussian.  Net result:  A (pseudo)Voight for peaks often works.  One
issue is what to do about the post-white-line peaks, which sometimes
are viewed as the first EXAFS wiggles.  Manceau has a nice paper about
S XANES  (I don't have the ref handy right now) in which he goes
through peak fitting and evaluates its uniqueness.
   mam

On Thu, Dec 8, 2016 at 5:40 AM, Matt Newville
 wrote:
> Hi Stephanie,
>
>
>
> On Wed, Dec 7, 2016 at 12:33 PM, Stephanie Laga 
> wrote:
>>
>> Dear all,
>>
>> I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS data.
>> I have been using moved the peak fitting function in Athena to model the
>> XANES with an arctan background function and a series of gaussians.
>>
>> Looking through the literature I haven't seen too many specifics to using
>> this approach (rationale for choosing the widths of peaks or how to define
>> the background function). Similarly, doesn't seem to be much rationale for
>> choosing a 4 vs 5 peak fit for the XANES.
>>
>> My main question is then...1) Is there a rational for picking the
>> background function, specifically the height and width (can I let the height
>> vary or should I be keeping a constant arctan through all samples)?
>>
>> Any advice is greatly appreciated!
>>
>> Stephanie
>>
>
> Matthew answered quickly, but sort of changed the subject, suggesting a
> different analysis (LSQ) and then discussing some of the pitfalls of that
> approach.  Your original question is still worth discussing.
>
> There is not a whole lot of justification in using one particular shape for
> the background.  A step broadened as arctan, error function are common and
> seem to work well. Each has some theoretical explanation in that the
> integral of a series of Lorentzian gives an arc-tangent function while the
> integral of a series of Gaussians will give the error function. (If this is
> wrong, can someone please correct?).  If you think as the above edge
> spectrum as a series of finely spaced individual transitions, then these
> functions have some justification.Whether it actually works well in
> detail on a particular spectrum is a separate question.   FWIW, I've also
> seen people use (successfully) a single, very broad Lorentzian for the "main
> edge".
>
> The use of Lorentzians, Gaussians, Voigts, and PseudoVoigts is somewhat more
> justified in that those are how you would expect a single electronic
> transition to appear, especially broadened in the way(s) you'd expect a
> monochromatic X-ray beam to be energy broadened.  Using such functions is
> essentially asserting that there is a single electronic transition at that
> energy, and you want to know it's size and shape.  This is not wrong, but it
> does not inherently include any understanding of what that peak is. For
> pre-edge peaks, it's pretty well-justified, and works pretty well.  For
> peaks on or after the main edge or "white line", it's less justified because
> we know that EXAFS-like effects can be important.
>
> The biggest dangers in the peak-fitting approach are:
>1) one always gets an answer, and that is rarely "no, this is not the
> right model to use".  In fairness, most linear algebra methods used for
> XANES analysis or really most other spectroscopies have the same feature.
>2) interpretation of the results can be challenging, or at least it is
> hard to know when they are misleading.  Again, most linear algebra methods
> used for XANES analysis or really most other spectroscopies have the same
> feature.
>3) it can sort of willfully ignore other parts of the spectra.  In
> fairness, we all do this sort of thing all the time.
>
> Hope that helps.  Peak fitting is not exactly "theoretical XANES analysis",
> but it is not always done in an ad-hoc manner out of ignorance either.
>
> Linear algebra techniques are completely justified too.
>
> Hope that helps,
>
> --Matt Newville
>
>
>
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Re: [Ifeffit] Peakfitting CeO2 data in Athena

[Matt Newville]

Hi Stephanie,



On Wed, Dec 7, 2016 at 12:33 PM, Stephanie Laga 
wrote:

> Dear all,
>
> I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS data. I
> have been using moved the peak fitting function in Athena to model the
> XANES with an arctan background function and a series of gaussians.
>
> Looking through the literature I haven't seen too many specifics to using
> this approach (rationale for choosing the widths of peaks or how to define
> the background function). Similarly, doesn't seem to be much rationale for
> choosing a 4 vs 5 peak fit for the XANES.
>
> My main question is then...1) Is there a rational for picking the
> background function, specifically the height and width (can I let the
> height vary or should I be keeping a constant arctan through all samples)?
>
> Any advice is greatly appreciated!
>
> Stephanie
>
>
Matthew answered quickly, but sort of changed the subject, suggesting a
different analysis (LSQ) and then discussing some of the pitfalls of that
approach.  Your original question is still worth discussing.

There is not a whole lot of justification in using one particular shape for
the background.  A step broadened as arctan, error function are common and
seem to work well. Each has some theoretical explanation in that the
integral of a series of Lorentzian gives an arc-tangent function while the
integral of a series of Gaussians will give the error function. (If this is
wrong, can someone please correct?).  If you think as the above edge
spectrum as a series of finely spaced individual transitions, then these
functions have some justification.Whether it actually works well in
detail on a particular spectrum is a separate question.   FWIW, I've also
seen people use (successfully) a single, very broad Lorentzian for the
"main edge".

The use of Lorentzians, Gaussians, Voigts, and PseudoVoigts is somewhat
more justified in that those are how you would expect a single electronic
transition to appear, especially broadened in the way(s) you'd expect a
monochromatic X-ray beam to be energy broadened.  Using such functions is
essentially asserting that there is a single electronic transition at that
energy, and you want to know it's size and shape.  This is not wrong, but
it does not inherently include any understanding of what that peak is. For
pre-edge peaks, it's pretty well-justified, and works pretty well.  For
peaks on or after the main edge or "white line", it's less justified
because we know that EXAFS-like effects can be important.

The biggest dangers in the peak-fitting approach are:
   1) one always gets an answer, and that is rarely "no, this is not the
right model to use".  In fairness, most linear algebra methods used for
XANES analysis or really most other spectroscopies have the same feature.
   2) interpretation of the results can be challenging, or at least it is
hard to know when they are misleading.  Again, most linear algebra methods
used for XANES analysis or really most other spectroscopies have the same
feature.
   3) it can sort of willfully ignore other parts of the spectra.  In
fairness, we all do this sort of thing all the time.

Hope that helps.  Peak fitting is not exactly "theoretical XANES analysis",
but it is not always done in an ad-hoc manner out of ignorance either.

Linear algebra techniques are completely justified too.

Hope that helps,

--Matt Newville
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Re: [Ifeffit] Peakfitting CeO2 data in Athena

[Matthew Marcus]

Ce(OH)4 is probably not a well-defined compound.  I wouldn't use it.  I suspect that 
"Ce(OH)4" is really hydrated CeO2 nanos.  I've measured 30nm CeO2 nanos and 
they look like bulk.
mam

On 12/7/2016 11:53 AM, Stephanie Laga wrote:

I had started with LSQ but switched to peak fitting because I was worried about 
the Ce(IV) reference. I have data for bulk CeO2 and Ce(OH)4, but doesn't this 
have some Ce(III) impurity in it? I'm not quite sure how to account for this 
when I do LSQ.

Another challenge I've had is in using the Ce(IV) refs for our nanoparticles, 
which are about 2-5 nm in diameter. Is there a good Ce(IV) ref for nanos that 
are in this size range?

On Wed, Dec 7, 2016 at 2:37 PM, Matthew Marcus mailto:mamar...@lbl.gov>> wrote:

Instead of doing a bunch of peak fitting, try LSQ.  Use CeO2 (bulk or 
nanos) for one reference and some Ce(III) for the other.  Consistency check: 
see that the Ce(III) fraction is consistent over some set of Ce(III) references.
Ce(III) has an assymetric white line, so it doesn't really fit a single 
gaussian.  CeO2, unlike other Ce(IV), has a shoulder on the first peak, and the 
first peak is shifted left a little with respect to other Ce(IV).
mam


On 12/7/2016 10:33 AM, Stephanie Laga wrote:

Dear all,

I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS 
data. I have been using moved the peak fitting function in Athena to model the 
XANES with an arctan background function and a series of gaussians.

Looking through the literature I haven't seen too many specifics to 
using this approach (rationale for choosing the widths of peaks or how to 
define the background function). Similarly, doesn't seem to be much rationale 
for choosing a 4 vs 5 peak fit for the XANES.

My main question is then...1) Is there a rational for picking the 
background function, specifically the height and width (can I let the height 
vary or should I be keeping a constant arctan through all samples)?

Any advice is greatly appreciated!

Stephanie


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Re: [Ifeffit] Peakfitting CeO2 data in Athena

[Stephanie Laga]

I had started with LSQ but switched to peak fitting because I was worried
about the Ce(IV) reference. I have data for bulk CeO2 and Ce(OH)4, but
doesn't this have some Ce(III) impurity in it? I'm not quite sure how to
account for this when I do LSQ.

Another challenge I've had is in using the Ce(IV) refs for our
nanoparticles, which are about 2-5 nm in diameter. Is there a good Ce(IV)
ref for nanos that are in this size range?

On Wed, Dec 7, 2016 at 2:37 PM, Matthew Marcus  wrote:

> Instead of doing a bunch of peak fitting, try LSQ.  Use CeO2 (bulk or
> nanos) for one reference and some Ce(III) for the other.  Consistency
> check: see that the Ce(III) fraction is consistent over some set of Ce(III)
> references.
> Ce(III) has an assymetric white line, so it doesn't really fit a single
> gaussian.  CeO2, unlike other Ce(IV), has a shoulder on the first peak, and
> the first peak is shifted left a little with respect to other Ce(IV).
> mam
>
>
> On 12/7/2016 10:33 AM, Stephanie Laga wrote:
>
>> Dear all,
>>
>> I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS
>> data. I have been using moved the peak fitting function in Athena to model
>> the XANES with an arctan background function and a series of gaussians.
>>
>> Looking through the literature I haven't seen too many specifics to using
>> this approach (rationale for choosing the widths of peaks or how to define
>> the background function). Similarly, doesn't seem to be much rationale for
>> choosing a 4 vs 5 peak fit for the XANES.
>>
>> My main question is then...1) Is there a rational for picking the
>> background function, specifically the height and width (can I let the
>> height vary or should I be keeping a constant arctan through all samples)?
>>
>> Any advice is greatly appreciated!
>>
>> Stephanie
>>
>>
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Re: [Ifeffit] Peakfitting CeO2 data in Athena

[Matthew Marcus]

Instead of doing a bunch of peak fitting, try LSQ.  Use CeO2 (bulk or nanos) 
for one reference and some Ce(III) for the other.  Consistency check: see that 
the Ce(III) fraction is consistent over some set of Ce(III) references.
Ce(III) has an assymetric white line, so it doesn't really fit a single 
gaussian.  CeO2, unlike other Ce(IV), has a shoulder on the first peak, and the 
first peak is shifted left a little with respect to other Ce(IV).
mam

On 12/7/2016 10:33 AM, Stephanie Laga wrote:

Dear all,

I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS data. I 
have been using moved the peak fitting function in Athena to model the XANES 
with an arctan background function and a series of gaussians.

Looking through the literature I haven't seen too many specifics to using this 
approach (rationale for choosing the widths of peaks or how to define the 
background function). Similarly, doesn't seem to be much rationale for choosing 
a 4 vs 5 peak fit for the XANES.

My main question is then...1) Is there a rational for picking the background 
function, specifically the height and width (can I let the height vary or 
should I be keeping a constant arctan through all samples)?

Any advice is greatly appreciated!

Stephanie


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[Ifeffit] Peakfitting CeO2 data in Athena

[Stephanie Laga]

Dear all,

I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS data. I
have been using moved the peak fitting function in Athena to model the
XANES with an arctan background function and a series of gaussians.

Looking through the literature I haven't seen too many specifics to using
this approach (rationale for choosing the widths of peaks or how to define
the background function). Similarly, doesn't seem to be much rationale for
choosing a 4 vs 5 peak fit for the XANES.

My main question is then...1) Is there a rational for picking the
background function, specifically the height and width (can I let the
height vary or should I be keeping a constant arctan through all samples)?

Any advice is greatly appreciated!

Stephanie
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